From chemistry-request@server.ccl.net Fri Jun 14 02:21:21 2002 Received: from sungod.ccs.yorku.ca ([130.63.236.104]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5E6LLe12012 for ; Fri, 14 Jun 2002 02:21:21 -0400 Received: from curl.gkcl.yorku.ca (curl.gkcl.yorku.ca [130.63.232.224]) by sungod.ccs.yorku.ca (8.9.3/8.9.3) with ESMTP id CAA18719 for ; Fri, 14 Jun 2002 02:21:21 -0400 (EDT) Received: (from chan@localhost) by curl.gkcl.yorku.ca (8.10.0/8.10.0) id g5E6LK406815 for chemistry@ccl.net; Fri, 14 Jun 2002 02:21:20 -0400 (EDT) From: Wai-To Chan Message-Id: <200206140621.g5E6LK406815@curl.gkcl.yorku.ca> Subject: Thermal corrections To: chemistry@ccl.net Date: Fri, 14 Jun 2002 02:21:19 -0400 (EDT) X-Mailer: ELM [version 2.5 PL3] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit There is a paper "Thermochemistry in Gaussian" by Joseph W. Ochterski at Gaussian Inc which may be helpful. The paper is probably still available > from the gaussian homepage. I suppose you didn't save the checkpoint file. There is this utility program freqchk which I've never used in the g98 package that may do what you want if you have the check file. I have a simple fortran code that can restore thermochemical quantities including H and G from a g98 frequency output file (default printing option required) at specified temperature. A while ago I posted the code in response to a similar question. Email me if you need it and I will repost it. Wai-To Chan <<<<<<<<<<<<<<<<<<<<<<,,,, From: "David J Anick" To: chemistry@ccl.net Subject: Thermal corrections Date: Thu, 13 Jun 2002 14:17:08 -0700 Dear CCLers, Having completed a Gaussian98 frequencies/ZPE calculation at an optimized geometry, I now find that I would like to know the thermal corrections to energy, enthalpy and Gibbs free energy at a different temperature (77 K) than the one that Gaussian98 automatically calculated (298 K). I don't want to re-run the calculation if possible because it took nearly a week. Can anyone tell me the formula(s) that Gaussian98 uses to compute these data? If it involves integrating Cp or Cp/T, how do I obtain Cp as a function of temperature? Thank you in advance, David Anick MD PhD David.Anick@gte.net >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> From chemistry-request@server.ccl.net Fri Jun 14 03:02:25 2002 Received: from kc-msxproto2.kc.umkc.edu ([134.193.143.159]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5E72Pe12407 for ; Fri, 14 Jun 2002 03:02:25 -0400 Received: from mkc-24-166-189-59.kc.rr.com ([24.166.189.59]) by kc-msxproto2.kc.umkc.edu with Microsoft SMTPSVC(5.0.2195.4453); Fri, 14 Jun 2002 02:02:25 -0500 Subject: CCL:Thermal corrections From: Dave Harris To: chemistry@ccl.net Cc: David J Anick Content-Type: text/plain Content-Transfer-Encoding: 7bit X-Mailer: Evolution/0.13 (Preview Release) Date: 14 Jun 2002 02:54:51 -0400 Message-Id: <1024037700.6457.10.camel@dhcp-521-27> Mime-Version: 1.0 X-OriginalArrivalTime: 14 Jun 2002 07:02:25.0343 (UTC) FILETIME=[7023ECF0:01C21371] On Thu, 2002-06-13 at 17:17, David J Anick wrote: > > Dear CCLers, > > Having completed a Gaussian98 frequencies/ZPE calculation > at an optimized geometry, I now find that I would like to know > the thermal corrections to energy, enthalpy and Gibbs free > energy at a different temperature (77 K) than the one that > Gaussian98 automatically calculated (298 K). > > I don't want to re-run the calculation if possible because > it took nearly a week. If you still have either a checkpoint (.chk) file or a formatted checkpoint (.fchk) file produced by the original frequency calculation, you can use the freqchk utility to calculate thermodynamic parameters for different temperatures, pressures, and isotope masses. It can also be used to change the scaling factor applied to calculated vibrational frequencies. Info from Gaussian is at: > Can anyone tell me the formula(s) that Gaussian98 uses > to compute these data? This can also be found at the Gaussian site: Regards, -- Dave Harris Department of Chemistry University of Missouri-Kansas City From chemistry-request@server.ccl.net Fri Jun 14 08:14:36 2002 Received: from postoffice.mail.cornell.edu ([132.236.56.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5ECEae16706 for ; Fri, 14 Jun 2002 08:14:36 -0400 Received: from cornell.edu ([128.84.182.122]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id IAA04918 for ; Fri, 14 Jun 2002 08:14:31 -0400 (EDT) Sender: richard@cornell.edu Message-ID: <3D09DE23.53AAE90D@cornell.edu> Date: Fri, 14 Jun 2002 08:14:27 -0400 From: Richard Gillilan X-Mailer: Mozilla 4.77 [en] (X11; U; Linux 2.4.16 i686) X-Accept-Language: en MIME-Version: 1.0 CC: chemistry@ccl.net Subject: CCL:OELib (was linux babel) References: <200206132055.NAA01766@haney.hbond.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit "Dr. David N. Haney" wrote: > > Actually, Babel has been made into an open source library. You can > compile it into a "BABEL" program or you can compile it into your > own software. It is now called "OELIB" and is available for download > > from OpenEye Scientific Software (http://www.eyesopen.com/download.html). > OpenBabel is apparently a branch off the original OELib source. There is a note in the documentation about OpenEye wanting to close their version but leave the OpenBabel source GPL'd. Anyone know what the differences are or what OpenEye has in mind for their code? ... is there something problematic about the OELib design which they want to change? Richard Gillilan MacCHESS, Cornell From chemistry-request@server.ccl.net Fri Jun 14 08:32:46 2002 Received: from ucidoor.unitedcatalysts.com ([208.23.162.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5ECWje16953 for ; Fri, 14 Jun 2002 08:32:45 -0400 Received: by ucidoor.unitedcatalysts.com; (8.8.8/1.3/10May95) id IAA15487; Fri, 14 Jun 2002 08:32:45 -0400 (EDT) Received: from 10.1.0.50 by ucismtp02.unitedcatalysts.com (InterScan E-Mail VirusWall NT); Fri, 14 Jun 2002 08:30:04 -0400 Received: from lvlxch01.unitedcatalysts.com ([10.16.100.88]) by lvlmail.unitedcatalysts.com (PMDF V6.0-24 #41777) with ESMTP id <0GXP00OKX3WKXM@lvlmail.unitedcatalysts.com>; Fri, 14 Jun 2002 08:26:44 -0400 (EDT) Received: by lvlxch01.unitedcatalysts.com with Internet Mail Service (5.5.2650.21) id ; Fri, 14 Jun 2002 08:30:10 -0400 Content-return: allowed Date: Fri, 14 Jun 2002 08:30:09 -0400 From: "Shobe, Dave" Subject: RE: CI calculation for CuO To: "'corrice@siue.edu'" , chemistry@ccl.net Message-id: <157A51F55AAAD3119CD70008C7B1629D01C15D9E@lvlxch01.unitedcatalysts.com> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g5ECWke16954 It would help us to know what kinds of problems you are having. Will the calculation start? Does the SCF not achieve convergence? Does the calculation stop after the 8th excited state? Etc. --David Shobe Süd-Chemie Inc. phone (502) 634-7409 fax (502) 634-7724 email dshobe@sud-chemieinc.com Don't bother flaming me: I'm behind a firewall. -----Original Message----- From: corrice@siue.edu [mailto:corrice@siue.edu] Sent: Thursday, June 13, 2002 3:58 PM To: chemistry@ccl.net Subject: CCL:CI calculation for CuO TO WHOM THIS MAY CONCERN: I WAS WONDERING WHAT WAS WRONG WITH THE WAY THIS INPUT FILE WAS SET UP FOR G98. I HAVE BEEN HAVE PROBLEMS WITH THIS PARTICULAR ONE. I HAVE TRIED DIFFERENT KEYWORDS BUT NOTHING SEEMS TO BE WORKING. THE INPUT FILE IS ATTACHED. COREY RICE SIUE CHEMISTRY DEPT. CORRICE@SIUE.EDU From chemistry-request@server.ccl.net Fri Jun 14 05:10:57 2002 Received: from mh1-cam.cam.accelrys.com ([192.190.183.253]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5E9Ave14623 for ; Fri, 14 Jun 2002 05:10:57 -0400 Received: from camdmail01.cam.accelrys.com ([172.27.160.90]) by mh1-cam.cam.accelrys.com with esmtp (Exim 3.12 #1 (Debian)) id 17In6Z-0002i6-00 for ; Fri, 14 Jun 2002 10:10:51 +0100 To: "chemistry@ccl.net" Subject: Accelrys Cerius2 Training in Cambridge, UK MIME-Version: 1.0 X-Mailer: Lotus Notes Release 5.0.9a January 7, 2002 Message-ID: From: tluu@accelrys.com Date: Fri, 14 Jun 2002 10:10:49 +0100 X-MIMETrack: Serialize by Router on camdmail01/Server/Accelrys(Release 5.0.9 |November 16, 2001) at 06/14/2002 09:10:49 AM, Serialize complete at 06/14/2002 09:10:49 AM Content-Type: multipart/alternative; boundary="=_alternative 00326D0E80256BD8_=" This is a multipart message in MIME format. --=_alternative 00326D0E80256BD8_= Content-Type: text/plain; charset="us-ascii" Accelrys Inc. will be holding two workshops involving the Cerius2 user interface at our office in Cambridge, UK, in July 2002. The "Introduction to Cerius2 for Life Sciences Workshop" will be offered on July 9-10. This course provides an overview of molecular modelling techniques for life sciences applications using Cerius2. The workshop will focus on basic skills for use of the interface and will explore various modules in the areas of rational-drug design, structure-based drug design, and combinatorial chemistry. Prior modelling experience is not assumed making this course a great place to learn molecular modelling with Cerius2. On July 11-12, the "Library Design and Analysis Workshop" will be held. This course will cover the basics of combinatorial library design, from initial library specification through to library analysis techniques. Various approaches to library subsetting will be described, including methods to select chemically diverse subsets from a virtual library, as well as techniques for lead explosion, after initial SAR data has been determined. Other topics covered will include methods for library-library comparison and several approaches to hole-filling of an existing library. Familiarity with the Cerius2 environment is required for attendance to this workshop. Fees for each 2-day course are GBP 850 commercial, GBP 620 government, and GBP 450 academic. Registration is on-line at URL http://www.accelrys.com/training/rdd/registration.php. Further detailed information about this and other Accelrys training workshops can be found at the Accelrys website (http://www.accelrys.com/training/rdd/schedule.html). Please do not hesitate to contact us should you have any questions. Thank you very much. Tien Luu +44 1223 228 608 Judith Madeley +44 1223 228 609 --=_alternative 00326D0E80256BD8_= Content-Type: text/html; charset="us-ascii"
Accelrys Inc. will be holding two workshops involving the Cerius2 user
interface at our office in Cambridge, UK, in July 2002.

The "Introduction to Cerius2 for Life Sciences Workshop" will be offered on
July 9-10.  This course provides an overview of molecular modelling
techniques for life sciences applications using Cerius2.  The workshop will
focus on basic skills for use of the interface and will explore various
modules in the areas of rational-drug design, structure-based drug design,
and combinatorial chemistry.  Prior modelling experience is not assumed
making this course a great place to learn molecular modelling with Cerius2.

On July 11-12, the "Library Design and Analysis Workshop" will be held.
This course will cover the basics of combinatorial library design, from
initial library specification through to library analysis techniques.
Various approaches to library subsetting will be described, including
methods to select chemically diverse subsets from a virtual library, as well
as techniques for lead explosion, after initial SAR data has been
determined. Other topics covered will include methods for library-library
comparison and several approaches to hole-filling of an existing library.
Familiarity with the Cerius2 environment is required for attendance to this
workshop.

Fees for each 2-day course are GBP 850 commercial, GBP 620 government,
and GBP 450 academic.

Registration is on-line at URL
http://www.accelrys.com/training/rdd/registration.php.  Further detailed
information about this and other Accelrys training workshops can be found
at the Accelrys website
(http://www.accelrys.com/training/rdd/schedule.html).

Please do not hesitate to contact us should you have any questions.

Thank you very much.

Tien Luu
+44 1223 228 608
Judith Madeley
+44 1223 228 609





 --=_alternative 00326D0E80256BD8_=-- From chemistry-request@server.ccl.net Thu Jun 13 22:59:54 2002 Received: from sina.com ([202.108.35.253]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g5E2xre10203 for ; Thu, 13 Jun 2002 22:59:54 -0400 Received: (qmail 21370 invoked by uid 99); 14 Jun 2002 02:52:43 -0000 Message-ID: <20020614025243.21368.qmail@sina.com> From: kzong To: CHEMISTRY@ccl.net Subject: some questions about charmm MIME-Version: 1.0 Date: Fri, 14 Jun 2002 10:52:43 +0800 X-Mailer: SinaMail 3.0Beta (FireToad) X-Priority: 3 Dear all: I have two questions about charmm: 1. When I execute my MD simulation, I get the error message "ENERGY CHANGE TOLERANCE EXCEEDED" after hundreds of steps. What's the matter and how to resolve it? 2. When I use "crystal" subcommand to define a crystal and then execute a MD simulation with periodic boundary condiction. I find that the size of system is changed during the simulate process. Can I fix it? =================================================================== From chemistry-request@server.ccl.net Fri Jun 14 08:55:52 2002 Received: from mail1-0.chcgil.ameritech.net ([206.141.192.68]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5ECtpe17690 for ; Fri, 14 Jun 2002 08:55:52 -0400 Received: from localhost ([66.73.198.128]) by mail1-0.chcgil.ameritech.net (InterMail vM.4.01.02.17 201-229-119) with ESMTP id <20020614125551.FREM346.mail1-0.chcgil.ameritech.net@localhost>; Fri, 14 Jun 2002 07:55:51 -0500 Date: Fri, 14 Jun 2002 07:55:47 -0500 Subject: Re: CCL:OELib (was linux babel) Content-Type: text/plain; charset=US-ASCII; format=flowed Mime-Version: 1.0 (Apple Message framework v482) Cc: chemistry@ccl.net To: Richard Gillilan From: Geoff Hutchison In-Reply-To: <3D09DE23.53AAE90D@cornell.edu> Message-Id: <0C1D9954-7F96-11D6-BDF2-0050E4863261@wso.williams.edu> Content-Transfer-Encoding: 7bit X-Mailer: Apple Mail (2.482) On Friday, June 14, 2002, at 07:14 AM, Richard Gillilan wrote: > Anyone know what the differences are or what OpenEye has > in mind for their code? ... is there something problematic > about the OELib design which they want to change? I hate to speak for other people, but I can shed at least a little light on this. OpenEye is rewriting a new "OEChem" library, which will not be GPL'ed. Of course the *existing* OELib will be under the GPL--you can't retroactively change a license. But OELib will not be maintained. "Matthew Stahl" wrote: > We've pretty much stopped development beyond that, although what is > already GPL'ed will stay GPL'ed. ... > The library we're building is no longer called OELib - it is now > OEChem. We > will probably not revert back to GPL b/c the GPL doesn't protect us from > having our competitors use the code in certain circumstances. Open Babel exists with the blessing of Matt Stahl, OpenEye and company. The differences between the 1.99 release and OELib are pretty small. The current version in development contains quite a few fixes, new features and new file formats including support for CML. For more information, including the Open Babel roadmap, see or check out the openbabel-discuss mailing list from the webpage. ------- -Geoff Hutchison Ratner/Marks Groups (847) 491-3295 Northwestern Chemistry http://www.chem.nwu.edu/ From chemistry-request@server.ccl.net Fri Jun 14 09:16:13 2002 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5EDGDe17906 for ; Fri, 14 Jun 2002 09:16:13 -0400 Received: from arlen.ccl.net (arlen.ccl.net [192.148.249.10]) by ccl.net (8.11.6+Sun/8.11.6/OSC 2.0) with ESMTP id g5EDGEe16014; Fri, 14 Jun 2002 09:16:14 -0400 (EDT) Date: Fri, 14 Jun 2002 09:16:11 -0400 (EDT) From: Jan Labanowski To: chemistry@ccl.net cc: jkl@ccl.net Subject: CCL spam defences and what to do if your mail is rejected Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL subscribers... First, I wanted to thank those of you who recently helped my by sending the donations and orders. I am processing them busily. For those who still wonder if this is time to help, please see if you can be lured into it by reading my sponsorship pages available as links from our home page: http://www.ccl.net I wanted to tell you about our measures to fight spam. CCL is famous and usually receives a few hundred stupid, often offending, spam messages a day. We have many filters to catch them. Initially humans were scanning all suspected mail. (Sometimes humans were making mistakes, and clicked on the wrong button, but it was rare). The spam and virus situation is going out of control. I do not want to go into details, but only want to warn you that you may be even getting spam mail which presents itself as coming from CCL or from me personally (some people already complained). When you analyze header lines of your message (Received: records) you will discover that the From: line is forged, and that ccl.net or ccl.net domain was never in the path of the message. Please note that in our setup the fact that the author is a subscriber to CCL is not a factor in distributing the message. While on first instinct you would say that this is the best way to ensure that only subscribers can post, believe me, it is not. You often post from different addresses then you are subscribed. Also, scores of suspected spammers are subscribing every day hoping that subscription will grant them rights to post the message. I have no resources and rights to run background checks on people. Moreover, the From: line of the message can be trivially forged. Manually scanning all CCL incoming mail can become a full time job. While we have a great Web based interface to do this, it is still a lot of work. So we decided to reject some messages without human reading them. We keep our own database of spammers (I know about commercial blacklists, and we may move in this direction, but this is not an easy decision for many reasons). We decided to block those C class subnets from which spam had come to CCL or to my private mailbox from posting to CCL. We are using the /etc/mail/access database of sendmail and place there the appropriate REJECT records. This has an unwanted consequence... Some innocent civilians are being hurt. If you belong to ISP which allows spammers to send junk mail, you may end up not being able to post messages to CCL, since they will be rejected. Note that many ISPs give people a chance to "try for free". This is anonymous access which which spammers often use to send garbage mail. And you may belong to the ISP which does this (many big ones do, like AOL, for example). If your mail gets rejected from CCL, first send the bounce to my address at jkl@ccl.net (which I still do not block). Also, try to send a message from some other address. We are overzealous and "one strike you are out", but we will gladly put you back. If we do not know about the problem, we cannot resolve it. I am sorry if you are having problems, but it seems that we will soon lock ourselves in cages, and criminals will be running free. Jan Jan K. Labanowski | phone: 614-292-9279, FAX: 614-292-7168 Ohio Supercomputer Center | Internet: jkl@ccl.net 1224 Kinnear Rd, | http://www.ccl.net/chemistry.html Columbus, OH 43212-1163 | http://www.ccl.net/ From chemistry-request@server.ccl.net Fri Jun 14 12:42:11 2002 Received: from mail.isg.siue.edu ([146.163.5.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5EGgBe21622 for ; Fri, 14 Jun 2002 12:42:11 -0400 Received: from WEBSHIELD2.isg.siue.edu (webshield2.isg.siue.edu [146.163.5.150]) by mail.isg.siue.edu (8.9.1/8.9.1) with SMTP id LAA21530 for ; Fri, 14 Jun 2002 11:42:06 -0500 (CDT) Received: FROM mail.isg.siue.edu BY WEBSHIELD2.isg.siue.edu ; Fri Jun 14 11:42:05 2002 -0500 Received: from cougar.isg.siue.edu (cougar [146.163.5.29]) by mail.isg.siue.edu (8.9.1/8.9.1) with ESMTP id LAA21412 for ; Fri, 14 Jun 2002 11:42:00 -0500 (CDT) Received: from localhost (corrice@localhost) by cougar.isg.siue.edu (8.9.1/8.9.1) with ESMTP id LAA25280 for ; Fri, 14 Jun 2002 11:41:59 -0500 (CDT) Date: Fri, 14 Jun 2002 11:41:59 -0500 (CDT) From: COREY ALLEN RICE To: chemistry@ccl.net Subject: Re: CCL:CI calculation for CuO In-Reply-To: <200206141639.LAA25052@cougar.isg.siue.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Corey A Rice Southern Illinois University at Edwardsville Chemistry Department corrice@siue.edu http://www.siue.edu/~corrice On Fri, 14 Jun 2002 corrice@siue.edu wrote: > THE OUTPUT IS NOW ATTACHED TO THIS EMAIL. > THANK YOU FOR YOUR HELP. > > Quoting corrice@siue.edu: > > > TO WHOM THIS MAY CONCERN: > > > > I WAS WONDERING WHAT WAS WRONG WITH THE WAY THIS INPUT FILE WAS SET UP FOR > > G98. I HAVE BEEN HAVE PROBLEMS WITH THIS PARTICULAR ONE. I HAVE TRIED > > DIFFERENT KEYWORDS BUT NOTHING SEEMS TO BE WORKING. > > THE INPUT FILE IS ATTACHED. > > > > COREY RICE > > SIUE > > CHEMISTRY DEPT. > > CORRICE@SIUE.EDU > > > > From chemistry-request@server.ccl.net Fri Jun 14 16:07:08 2002 Received: from hsc.usf.edu ([131.247.67.157]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g5EK77e24499 for ; Fri, 14 Jun 2002 16:07:08 -0400 Received: through eSafe SMTP Relay 1022858817; Fri Jun 14 16:02:07 2002 Received: from mindless.com (out.moffitt.usf.edu [131.247.182.200]) by hsc.usf.edu (8.9.3+Sun/8.9.3) with ESMTP id QAA22101 for ; Fri, 14 Jun 2002 16:07:07 -0400 (EDT) Message-ID: <3D0A4CF1.CCF1D3EA@mindless.com> Date: Fri, 14 Jun 2002 16:07:13 -0400 From: David Smith X-Mailer: Mozilla 4.78 [en] (Win95; U) X-Accept-Language: en MIME-Version: 1.0 To: CCL Subject: build pdb's? Responses References: <3D067015.90BDDB0B@mindless.com> <004901c211da$91740e00$424f959f@Villa> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit A few of you asked to see the responses I got, they are shown below. Thanks for everyones input. If in one knows if any other free software please let me know. Thanks, David Smith ------------------------ > Hello CCL'ers, > > Does anyone know of a windows based freeware that allows one to build > pdb files from scratch. > > Thanks to all, > > David > ------------------------ Weblab lite viewer (accelrys.com) will import files in a variety of formats and export in PDB, among others. It has a quick-3D build, so you could draw a structure in ISIS Draw (free), save as a molfile, import to Weblab, and export as pdb. Most structures built that way would need modeling... Babel will also convert many more filetypes, but it has limited "modeling" You might check something like Tinker, for doing the modeling. >From this molfile: -ISIS- 06110217412D 23 26 0 0 0 0 0 0 0 0999 V2000 -2.7473 -0.0666 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7484 -0.8940 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0336 -1.3069 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0354 0.3461 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3200 -0.0630 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3198 -0.8940 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5297 0.1940 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0410 -0.4781 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -0.5315 -1.1539 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -0.1934 -1.9124 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6363 -2.0015 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1268 -1.3257 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7876 -0.5608 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 1.2713 0.1075 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0919 0.0196 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5754 0.6871 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2385 1.4411 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4133 1.5236 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9335 0.8551 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4618 0.3457 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -3.4620 1.1707 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1762 -0.0670 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8786 0.9292 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2 3 1 0 0 0 0 8 13 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 3 6 2 0 0 0 0 13 14 1 0 0 0 0 6 9 1 0 0 0 0 14 15 2 0 0 0 0 8 7 1 0 0 0 0 15 16 1 0 0 0 0 7 5 1 0 0 0 0 16 17 2 0 0 0 0 8 9 1 0 0 0 0 17 18 1 0 0 0 0 1 2 2 0 0 0 0 18 19 2 0 0 0 0 19 14 1 0 0 0 0 5 4 2 0 0 0 0 1 20 1 0 0 0 0 4 1 1 0 0 0 0 20 21 1 0 0 0 0 5 6 1 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 M END I generated this pdb file from weblab: REMARK Accelrys ViewerPro PDB file REMARK Created: Tue Jun 11 17:41:21 Pacific Daylight Time 2002 ATOM 1 C1 MOL 1 6.797 -7.842 -0.066 1.00 0.00 ATOM 2 C2 MOL 1 6.835 -9.225 -0.278 1.00 0.00 ATOM 3 C3 MOL 1 8.025 -9.941 -0.154 1.00 0.00 ATOM 4 C4 MOL 1 7.955 -7.143 0.269 1.00 0.00 ATOM 5 C5 MOL 1 9.133 -7.863 0.385 1.00 0.00 ATOM 6 C6 MOL 1 9.164 -9.225 0.183 1.00 0.00 ATOM 7 C7 MOL 1 10.492 -7.326 0.747 1.00 0.00 ATOM 8 C8 MOL 1 11.323 -8.478 0.059 1.00 0.00 ATOM 9 C9 MOL 1 10.531 -9.726 0.413 1.00 0.00 ATOM 10 C10 MOL 1 11.003 -10.975 -0.327 1.00 0.00 ATOM 11 C11 MOL 1 12.485 -11.208 0.088 1.00 0.00 ATOM 12 C12 MOL 1 13.368 -9.965 -0.276 1.00 0.00 ATOM 13 C13 MOL 1 12.832 -8.677 0.424 1.00 0.00 ATOM 14 C14 MOL 1 13.798 -7.501 0.144 1.00 0.00 ATOM 15 C15 MOL 1 15.155 -7.778 0.011 1.00 0.00 ATOM 16 C16 MOL 1 16.067 -6.755 -0.226 1.00 0.00 ATOM 17 C17 MOL 1 15.629 -5.441 -0.332 1.00 0.00 ATOM 18 C18 MOL 1 14.276 -5.154 -0.203 1.00 0.00 ATOM 19 C19 MOL 1 13.369 -6.181 0.035 1.00 0.00 ATOM 20 C20 MOL 1 5.499 -7.090 -0.191 1.00 0.00 ATOM 21 C21 MOL 1 5.288 -6.248 1.082 1.00 0.00 ATOM 22 C22 MOL 1 4.311 -8.044 -0.428 1.00 0.00 ATOM 23 C23 MOL 1 5.623 -6.090 -1.355 1.00 0.00 TER If you want residue info, etc, I doubt you'll find anything free besides some modeling program like ECEPP. --------------------------------- ArgusLab will write PDB files for any structure you can construct. ArgusLab is not free, but it's darned inexpensive (probably less than what an average Seattle coffee junkie spends on latte's and biscotti at Starbucks each month :) You can obtain ArgusLab at http://www.arguslab.com Cheers, Mark Thompson --------------------------------- Dear David, Try our program VEGA (http://users.unimi.it/~ddl). It is really free!!! Best regards Giulio Vistoli --------------------------------- David, May not be of use to you, but Molekel (http://www.cscs.ch/molekel/) allows you to build PDB files from many types of input (including, i think, XYZ files which are easy to build by hand). At any rate, I would be interested in hearing a summary of responses. Best regards, Gary ------------------------------- DH From chemistry-request@server.ccl.net Fri Jun 14 18:15:33 2002 Received: from ivory.trentu.ca ([192.75.12.103]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5EMFXe25776 for ; Fri, 14 Jun 2002 18:15:33 -0400 Received: from trentu.ca ([206.248.117.30]) by trentu.ca (PMDF V5.2-32 #37862) with ESMTP id <01KIXHXE6O7C0005F8@trentu.ca> for chemistry@ccl.net; Fri, 14 Jun 2002 18:15:09 EST Date: Fri, 14 Jun 2002 18:16:55 -0400 From: elewars Subject: direct scf and RAM To: chemistry@ccl.net Message-id: <3D0A6B57.99B812F1@trentu.ca> MIME-version: 1.0 X-Mailer: Mozilla 4.79 [en] (WinNT; U) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en 2002 June 14 Does it seem likely to everyone out there that the introduction of very big (and fast-access) electronic memories (RAM) will make direct SCF obsolete? Thanks E. Lewars ===== From chemistry-request@server.ccl.net Fri Jun 14 13:55:02 2002 Received: from mail.isg.siue.edu ([146.163.5.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5EHt2e22731 for ; Fri, 14 Jun 2002 13:55:02 -0400 Received: from WEBSHIELD1.isg.siue.edu (webshield1.isg.siue.edu [146.163.5.149]) by mail.isg.siue.edu (8.9.1/8.9.1) with SMTP id MAA21021 for ; Fri, 14 Jun 2002 12:54:56 -0500 (CDT) Received: FROM mail.isg.siue.edu BY WEBSHIELD1.isg.siue.edu ; Fri Jun 14 12:54:55 2002 -0500 Received: from cougar.isg.siue.edu (cougar [146.163.5.29]) by mail.isg.siue.edu (8.9.1/8.9.1) with ESMTP id MAA20946 for ; Fri, 14 Jun 2002 12:54:50 -0500 (CDT) Received: (from nobody@localhost) by cougar.isg.siue.edu (8.9.1/8.9.1) id MAA29311; Fri, 14 Jun 2002 12:54:50 -0500 (CDT) Date: Fri, 14 Jun 2002 12:54:50 -0500 (CDT) From: corrice@siue.edu Message-Id: <200206141754.MAA29311@cougar.isg.siue.edu> X-Authentication-Warning: cougar.isg.siue.edu: nobody set sender to corrice@siue.edu using -f To: chemistry@ccl.net Reply-To: corrice@siue.edu MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="-MOQ10240772909bb9098c4366aceedff1bd2504c74467" User-Agent: IMP/PHP3 Imap webMail Program 2.0.11 Sender: corrice@siue.edu X-Originating-IP: 146.163.155.168 Subject: CI calculations of CuO This message is in MIME format. ---MOQ10240772909bb9098c4366aceedff1bd2504c74467 Content-Type: text/plain Content-Transfer-Encoding: 8bit SORRY EVERYONE ABOUT THE ATTACHMENTS. HERE THEY ARE. THANKS AGAIN. COREY RICE SIUE CHEMISTRY DEPT. CORRICE@SIUE.EDU ---MOQ10240772909bb9098c4366aceedff1bd2504c74467 Content-Type: text/plain; name="CuO_excited.gjf" Content-Transfer-Encoding: 8bit Content-Disposition: inline; filename="CuO_excited.gjf" %mem=210Mb #p UCI=(TransitionDensities,maxcycle=800,NStates=50)/6-311G(d) FormCheck=(All) Pop=(NPA,Regular) scf=(QC,maxcycle=800) IOp(9/40=5) > from cuo 0 2 O 0 -1.013351 -0.285889 0.293335 Cu 0 1.013336 0.285889 -0.293320 ---MOQ10240772909bb9098c4366aceedff1bd2504c74467 Content-Type: application/octet-stream; name="CuO_excited.out" Content-Transfer-Encoding: base64 Content-Disposition: inline; filename="CuO_excited.out" IEVudGVyaW5nIExpbmsgMSA9IEM6XEc5OFdcbDEuZXhlIFBJRD0gICAgICAxODQwLg0KICANCiBD b3B5cmlnaHQgKGMpIDE5ODgsMTk5MCwxOTkyLDE5OTMsMTk5NSwxOTk4IEdhdXNzaWFuLCBJbmMu DQogICAgICAgICAgICAgICAgICBBbGwgUmlnaHRzIFJlc2VydmVkLg0KICANCiBUaGlzIGlzIHBh cnQgb2YgdGhlIEdhdXNzaWFuKFIpIDk4IHByb2dyYW0uICBJdCBpcyBiYXNlZCBvbg0KIHRoZSBH 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